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R
Bash
Python
SQL

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Last updated on 2022-03-19.

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Halfdan Rydbeck



Profile

Recently developed a pipeline of rscripts to perform pathway and correlation network analysis of cord blood plasma proteomics data. Developed pipelines for automatic preprocessing and delivery of Illumina and Pacbio DNA sequencing output. Set up server infrastructure for NGS data handling. Manged NGS file servers, user access and data delivery. Examples of downstream analysis: Blasted an exon sequence against multiple assembled fish genomes to look for systematic loss in phylogeny. Analyzed bacterial methylomes, sequenced with Pacbio in, respect to virulens. PhD project. Developed an R package for clustering of genomic tracks. Scripts developed in R and The Genomic Hyperbrowser was used to study the dependencies and select genes, based on genomic, epigenomic and transcriptomic alterations in samples from osteosarcoma and immune cells. The gene expression, promoter methylation and DNA copy number data were acquired by oligonucleotide microarray technology, and the histone modification data was acquired by technology based on chromatin immune precipitation and next generation sequencing, ChIP-seq.

Research Experience

Researacher bioinformatics

Core Facilities Bioinformatics vid Sahlgrenska Akademin, Univeristy of Gothenburg

Göteborg, Sweden

2022 - 2020

  • Worked with Rstudio and the R package collections Bioconductor and Tidyverse. Reports where generated with R notebooks and the R package Bookdown. Github and GitKraken is used for code version control. Recently applied R packages are DEqMS for differential expression analysis of mass spectrometry data, WGCNA for proteins correlation analysis and ReactomeGSA for pathway analysis

Senior engineer bioinformatics

Norwegian Sequencing Center

University of Oslo, Norway

2017 - 2014

  • System setup, user management, data preprocessing, delivery and down stream analysis of Illumina and Pacbio sequence data at the Norwegian DNA sequencing center. Work

Principal engineer

Bioinformatics core facility

Rikshospitalet HF, Norway

2008 - 2007

  • Microarray gene expression analysis
  • Developing network-based methods to investigate and visualize clinically relevant patterns in data.

Research assistant

Human Genetics division

Children’s Hospital of Philadelphia, USA

2007 - 2006

  • Bash and scripting for data wrangling and testing Solar, Plink, TDT, Merlin, STATA, SAS, R
  • Work primarily done in R Shiny and Javascript (node and d3js).

Senior research assistant

Dept. of genetic epidemiology

A. I duPont Hospital for Children, USA

2005 - 2004

  • Used software for genetic linkage and association studies of diseases/syndroms Velocardiofacial Syndrome, ADHD, Neuroblastoma, Osteoporosis, Cornelia de Lange’s syndrome and Myopia • Solar, Plink, TDT, Merlin, STATA, SAS, R

Database coordinator

Human Genetics division

Children’s Hospital of Philadelphia, USA

2004 - 2002

  • Manged a database for SNP information Progeny2000

Teaching Experience

I like when teaching and learning is relaxing and joyfull

R for reprodicible scientific programming

Software carpentry

Oslo Norway

2018 - 2017

  • Covered introduction to R language for statistics applications
  • Graduate level class

Version controlling with git and github

Software carpentry

Oslo Norway

2018 - 2017

  • Topics covered from penalized regression to boosted trees and neural networks
  • Highest level course offered in department

Unix

Software carpentry

Oslo Norway

2018 - 2017

  • Covered modern statistical computing algorithms
  • 4th year PhD level class

Education

Sometimes I am almost tireless. This means that I fight hard so that the tasks or projects I undertake are completed on time and I do not give up until I’ve achieved the intended result

PhD bioinformatics

Medical faculty, University of Oslo

Oslo, Norway

2012 - 2007

  • • Thesis title: Integrative epigenome analysis • courses mostly statistics (30p) • Analysed gene expression, promoter methylation, histone occupancy and copynumber variation data with R and The Genomic Hyperbrwser. Developed and R package for clustering of genomic tracks.
  • University Graduate Fellow

Master of Science in Bioinformatics

Chalmers University of Technology

Gothenburg, Sweden

2001 - 2000

Master of Science in Molecular biology

University of Gothenburg /Uppsala

Göteborg/Uppsala, Sweden

1999 - 1993




Selected Publications, Posters, and Talks

References are availabel upon request

The proteome signature of cord blood plasma with high hematopoietic stem and progenitor cell count

Stem Cell Research

N/A

2022 - 2022

  • Authored with Anders K.Nilsson, Annika Thorsell, Sofia Frändberg,Helena Barreto Henriksson, Camilla Hesse, Gunnel Hellgren, Pia Lundgren, AnnHellström